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List:       bioconductor
Subject:    [BioC] enrichment packages that accept t-stat (or related stat) as input
From:       Gordon K Smyth <smyth () wehi ! EDU ! AU>
Date:       2013-08-30 12:51:33
Message-ID: Pine.WNT.4.64.1308302249190.7612 () PC975 ! wehi ! edu ! au
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Dear Juliet,

Why not use the enrichment functions that are already part of the limma 
package?   See

   ?roast
   ?camera
   ?romer

and references there-in.

Best wishes
Gordon


> Message: 19
> Date: Thu, 29 Aug 2013 20:43:04 -0400
> From: Juliet Hannah <juliet.hannah@gmail.com>
> To: Robert Castelo <robert.castelo@upf.edu>
> Cc: Bioconductor mailing list <bioconductor@r-project.org>
> Subject: Re: [BioC] enrichment packages that accept t-stat (or related
> 	stat) as input
> 
> Hi Robert,
> 
> Thanks for your response. I will look into it.
> 
> Also is it correct GSVA always requires an expression matrix. It seems 
> that it integrates with limma, so if I have done an analysis in limma 
> does this mean that I should be able to use GSVA for an enrichment 
> analysis.
> 
> Thanks,
> 
> Juliet
> 
> 
> On Thu, Aug 29, 2013 at 2:43 AM, Robert Castelo <robert.castelo@upf.edu>wrote:
> 
> > Juliet,
> > 
> > i think the first 5 pages in the vignette entitled "Using Categories to
> > Analyze Microarray Data" from the Category package:
> > 
> > http://www.bioconductor.org/**packages/release/bioc/html/**Category.html<http://www.bioconductor.org/packages/release/bioc/html/Category.html>
> >  
> > may be doing what you are looking for.
> > 
> > cheers,
> > robert.
> > 
> > 
> > On 08/28/2013 08:04 PM, Juliet Hannah wrote:
> > 
> > > All,
> > > 
> > > I am looking for an Bioconductor enrichment package that does something
> > > similar to GSEA for pre-computed test statistics. This method would not
> > > rely on a cutoff. That is, rather than passing an expression matrix, one
> > > can compute summarizes outside of the package (such as a limma t), and
> > > then
> > > pass these. Any suggestions?
> > > 
> > > Thanks,
> > > 
> > > Juliet
> > > 
> > > [[alternative HTML version deleted]]
> > > 
> > > ______________________________**_________________
> > > Bioconductor mailing list
> > > Bioconductor@r-project.org
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> > >  Search the archives: http://news.gmane.org/gmane.**
> > > science.biology.informatics.**conductor<http://news.gmane.org/gmane.science.biology.informatics.conductor>
> > >                 
> > > .
> > > 
> > > 
> > --
> > Robert Castelo, PhD
> > Associate Professor
> > Dept. of Experimental and Health Sciences
> > Universitat Pompeu Fabra (UPF)
> > Barcelona Biomedical Research Park (PRBB)
> > Dr Aiguader 88
> > E-08003 Barcelona, Spain
> > telf: +34.933.160.514
> > fax: +34.933.160.550
> > 
> 

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